[gmx-users] Berendsen Temperature Coupling and Heat
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 30 09:35:34 CEST 2008
Daniel S. Han wrote:
> I am running a steered MD simulation in an NPT ensemble using Berendsen
> thermostats. I expect that my system could heat up due to the external
> forces, and this heat would eventually be absorbed by the heat bath.
> I thought I could get an estimate of the heat released by looking at the
> Temperature (T) and lambda values (velocity scaling factors) available
> in the gromacs energy output files, but I wasn't sure I was calculating
> it correctly.
> Here's the algorithm I thought might work:
> at every time step, we have a Temperature (T) and a Lambda (L) taken
> from the edr output file.
> Where we can calculate the kinetic energy at any step as:
> Kinetic Energy (KE) = .5 * N_degrees_of_freedom * K_boltzman * T
> (which I'll call KE_output)
> If I understand correctly, KE_output is the result after scaling by
> Lambda^2. So if there were no temperature scaling, then the kinetic
> energy would be equal to:
> KE_no_scaling = KE_output / (lambda*lambda)
> Thus the heat exchanged between the system and the bath is:
> Heat = KE_output - KE_no_scaling
> where if heat is negative, it means that heat was released by the system
> and absorbed by the bath.
> Using this algorithm I found some odd results, where I found that both
> my Steered MD simulations and a simulation of the same system without
> external forces tended to absorb heat.
> I can post more details of that later, but for now, if anyone has any
> corrections/comments to this line of thought, it would be much appreciated.
It seems your appraoch is right. You can just plot lambda using
g_energy. If it less than one on average you are cooling, if it is more
than one you are heating the system.
If you integrate lambda - 1 you can compute the net heat flux into/out
of the system.
> Thanks in advance,
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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